From: Francesco Pietra (
Date: Sun Jul 01 2007 - 02:59:07 CDT

Must add that I have solved the issue of relating atoms in space to the "atom
serial number" with my MM package. Though, I would be happy to do that with VMD
because the MM package does not like much abridged pdb files. Of the molecule
in attachment, it shows correctly all atoms and connectivities, though for
chlorine it shows an isolated ball at the right place. MM relies on CONECT, not
atom radii.

--- Francesco Pietra <> wrote:

> Date: Sun, 1 Jul 2007 00:33:20 -0700 (PDT)
> From: Francesco Pietra <>
> Subject: atom serial number
> To: vmd <>
> The "small" organic molecule is at the forefront of my problems with MD, and
> I
> need to locate the atoms in space with respect to the "atom serial number" in
> pdb files.
> I have loaded into VMD 1.8.6 the molecule in attachment (which makes part of
> amber tutorials), I have printed the pdb file, noticed that it it is an
> abridged form of pdb file and that, even in this restricted form, it
> digresses
> from pdb rules (atom Cl, for chlorine, should be left-justified at column
> 13).
> This is no criticism, it is only to learn how to refine pdb files for my
> unpublished organic molecules in view of MD.
> As taking into account stereochemistry is a must in my studies, may I ask
> advice in locating the atoms in space through VMD 1.8.6? Though it is
> irrelevant to the case in attachment, this one will teach me how to deal with
> cases where stereochemical assignments are relevant.
> I have read about the "atom select" command of VMD. Is that the way? Is any
> possibility of graphical output on the VMD screen of the "atom serial
> number",
> or anything that can be related to that? In practice, I want to know which is
> which for H3/H4, F1/F2/F3, and so on.
> Thanks
> francesco pietra
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